- [Voiceover] Many of my colleagues focus on
excavating pyramids and giant temples and massive structures
but I’ve always been interested
in the archaeology of the invisible,
the archaeology of things you can’t see
but that do preserve over thousands of years.
And so as I started looking
at these microbes under a microscope,
at a certain moment I realized, wait a minute,
maybe we could recover some information
about the health and diet of people in the past.
(inquisitive music)
- [Swati] And how did this all start?
- You know, I was at the genomics conference
and I saw this incredible presentation
about Christina Warinner
and she was actually doing some interesting research
and I ended up corresponding with her.
Christina, great to meet you after all this time.
- I know, I'm so glad you could make it
and I can't wait to show you all of our research.
- [Jacques] So this is where the magic happens?
- [Christina] Yeah, right in here.
(suspenseful music)
- [Christina] The further we go into the lab,
we're still in part of an outer rim.
The further we go in,
the more precautions we take to control our own DNA.
And now we're suited up.
Let's go ahead and go inside.
- [Jacques] Oh, this is going to be exciting.
- [Swati] This is so cool.
Oh wow.
- We've laid out here one of our skeletons.
If we were to cut this bone in half,
we would see that all of the marrow inside
would be completely decomposed
and so what ends up happening
is that if you only have 1% human DNA,
you have to do an awful lot of sequencing
to get a human genome.
(suspenseful music)
- In calculus, 99% of what we find,
we do want.
- [Jacques] The DNA's pre-fragmented.
- It's pre-fragmented.
In fact, when we go through
ancient DNA library preparations,
we entirely skip that step.
It's already in the normal distribution,
it's already perfect for building libraries.
- It's a revolution in archaeology.
- And we're starting to reconstruct aspects
of diet and disease that we never had access to before
so it's an incredibly exciting time.
- So right now, we're in our sample collection room
within our ancient DNA laboratory
and we're going to collect dental calculus.
This tooth is approximately 4,000 years old
and right here we can see this is the root of a tooth.
This is the enamel crown.
And this along here, this is the dental calculus.
- [Jacques] So you can see why they call it calculus.
It's from the Greek word for stone.
- [Christina] You can see it forms a huge shelf,
which would have covered part of the gingiva.
So we're using a dental scaler tool here,
which we can use to just scrape down gently
on the dental calculus
and collect it into a sterile microtube.
We’ll now take this tube to the next room
where we will begin the process
of extracting DNA from this sample.
We’ll put this on a rotating mixer for about
three to four days and then when we’re done,
we’ll have DNA ready for extraction.
- [Swati] So Christina, how do you purify DNA?
- [Christina] We do this using a silica column
that allows us to bind DNA,
clean off all of the salts and other parts
of the buffers that we use.
(suspenseful music)
(calming music)
- What we see here is this is a tooth.
This is the tooth root and the dentin
and the top is the enamel crown.
We can zoom in a little bit more
and this is something that really jumped out at me.
Really fascinating when I first saw it
because this is incredible,
you can see that it’s layered in incremental layers
and that’s because that’s how calculus grows,
it forms incrementally.
So here we have an ordered record
of events and health information
throughout the life history of this individual.
So this is what it looks like when we stain the DNA
with a fluorescent dye.
Each point of light is an individual bacterial genome.
It’s glowing back at us.
It almost looks like a star field.
But this is what it looks like when you look at
millions of ancient bacterial genomes.
There’s nothing else in the archaeological record
that looks like this.
- [Jacques] That's interesting.
What are the implications for human health care?
- We had one question which was:
We know what causes periodontal disease today,
was it the same organisms that caused it in the past?
And we found that yes,
many of the same organisms that are implicated
in periodontal disease today are
the same ones we found in the past.
One of them is called Tannerella forsythia.
We had so many reads from this,
from this organism that we're able to reconstruct
a near complete genome.
- [Swati] So Christina, there are a few large gaps.
- We were so frustrated.
We couldn't figure out why we couldn't fill them.
We realized this is 48,000 consecutive bases
of antibiotic resistance genes
and our ancient genome simply lacked them.
- [Jacques] Did you find antibiotic resistance genes
in other organisms?
- We did find it in other ones
and that really demonstrates that antibiotic resistance,
although maybe not present at a high degree,
was present in the past just waiting for us
in the 20th century to select for it
with therapeutic antibiotics.
So we’re starting to learn that the oral microbiome
is intimately related both to local health within our mouth
and systemic health throughout our body.
So it affects things like cavities and periodontal disease
but it also was implicated in cardiovascular disease
and systemic inflammation.
How have behaviors in our modern lives altered
this relationship and maybe contributed to in,
to poor health today or more chronic disease?
We can go to specific points in the past,
ask specific questions, test these hypotheses,
and understand how we’re changing through time.
- You just never can tell how one single insight
can change a whole field.
- Yeah, and give you so much information,
not just about disease,
but also about the evolution of microbes.
- And its impact on human health.
(classical music)